https://github.com/bunpc/vasculardataviz
https://github.com/bunpc/vasculardataviz
Last synced: 5 months ago
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- Host: GitHub
- URL: https://github.com/bunpc/vasculardataviz
- Owner: BUNPC
- Created: 2019-11-19T16:28:15.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-08-13T23:50:58.000Z (almost 6 years ago)
- Last Synced: 2025-09-09T20:41:23.254Z (9 months ago)
- Size: 187 KB
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Discription:
This app helps to visualize pO2pts, stalling segments on angiogram and get branch order statistics for that data.
# input:
Angiogram volume
A file name is provided for a MAT or TIF file that contains the volumetric image of the angiogram. This is generally the angiogram image file and not a segmented angiogram.
Graph file
A file name is provided for a MAT file that contains the graph information with the following fields:
Graph.nodes [Nx3] - This is the 3D position of each of the N nodes in the graph
Graph.edges [Mx2] - This is the list of M edges giving the index for each of the 2 nodes connected by the given edge.
Graph.diam [Nx1] - This is the diameter at each node in units of micrometers.
Graph.nodeType [Nx1] - This indicates whether a node is an artery (1), a capillary (2), or a vein(3). This is optional in the input file.
Graph.segInfo - This is a data structure that contains information about the nodes and edges contained in each vascular segment.
OCT stall data
This is the output saved from capStallGUI.
The input has 5 variables:
Cap [Nx2] - contains 2D coordinates of the capillary stall points in the MIP coordinate system
Pts [Nx3] - contains 3D coordinates of the capillary stall points in the 3D average volume
Seg [Nx1]- is a structure data type.
Seg.pos [MX3]- contains positions of the capillary segment. Note that the number of node points M generally differs for each capillary segment.
Seg.mask [Px1] - contains a list of indices into the volume image indicating the voxels corresponding to the masked capillary segment.
Int_ts [N*T] - contains the intensity time series of each segment averaged over the list of Seg.mask voxels for the given segment.
StallingMatrix [N*T] - is binary matrix with stalls indicated as 1 and non-stalls as 0. This is the famous stall-o-gram.
N - number of stalling capillary segments
T - number of images in the time series
pO2 Data
This is pO2 points information
pO2pts [Nx3] - contains 3D coordinates of pO2 pts in the measured volume.
N - number of po2 pts measured
# Output:
Graph.pO2ptsBO -
Graph.IntrapO2ptspath -